Armour is indeed more effective in the long run, but if you want your char going around in leather, fur or other more barbaric stuff, Alteration flesh spells can be helpfull. The major drawback is the 1 minute duration. It's a real nuisance that it drops of that fast and you've to apply it again, which is very unwelcome during the thick of a fight.
Your suspicions are correct Joe.
Both heavy and light armor have a hidden armor bonus when you wear a full set. The armor cap in this game is 667, the hidden bonus for both light and heavy armor is 100 when wearing a full set (so if you have a displayed 567 and are wearing a complete set of heavy/light you're at max ac).
If you're running a mage with ebony flesh (300 with mage armor 3/3) then you basically have aprox 45% physical protection (300/667).